Merge remote-tracking branch 'origin/issues/79_status_output' into

hhund · hhund · commit 7c78c7a72f26 · 2022-07-12T10:09:45.000+02:00
develop
diff --git a/codex-process-data-transfer/pom.xml b/codex-process-data-transfer/pom.xml
@@ -45,7 +45,7 @@
 				<artifactId>maven-surefire-plugin</artifactId>
 				<configuration>
 					<excludes>
-						<exclude>**/ValidateDataLearningTest.java</exclude>
+						<exclude>**/*LearningTest.java</exclude>
 					</excludes>
 				</configuration>
 			</plugin>
diff --git a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/ConstantsDataTransfer.java b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/ConstantsDataTransfer.java
@@ -43,6 +43,7 @@ public interface ConstantsDataTransfer
 	String CODESYSTEM_NUM_CODEX_DATA_TRANSFER_VALUE_EXPORT_TO = "export-to";
 	String CODESYSTEM_NUM_CODEX_DATA_TRANSFER_VALUE_DATA_REFERENCE = "data-reference";
 	String CODESYSTEM_NUM_CODEX_DATA_TRANSFER_VALUE_DRY_RUN = "dry-run";
+	String CODESYSTEM_NUM_CODEX_DATA_TRANSFER_VALUE_ENCRYPTED_BUNDLE_SIZE = "encrypted-bundle-size";
 
 	String PROFILE_NUM_CODEX_TASK_DATA_TRIGGER_PROCESS_URI = "http://www.netzwerk-universitaetsmedizin.de/bpe/Process/dataTrigger/";
 	String PROFILE_NUM_CODEX_TASK_DATA_TRIGGER_PROCESS_URI_AND_LATEST_VERSION = PROFILE_NUM_CODEX_TASK_DATA_TRIGGER_PROCESS_URI
diff --git a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/service/receive/LogError.java b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/service/receive/LogError.java
@@ -71,13 +71,15 @@ protected void doExecute(DelegateExecution execution) throws BpmnError, Exceptio
 			task.addOutput(output);
 
 			if (CODESYSTEM_NUM_CODEX_DATA_TRANSFER_ERROR_SOURCE_VALUE_CRR.equals(errorSource))
-				logger.warn("Error while executing local process: code: '{}', message: {}", errorCode, errorMessage);
+				logger.error("Error while executing local process; code: '{}', message: {}", errorCode, errorMessage);
 			else
-				logger.warn("Error while executing process at {}: code: '{}', message: {}", errorSource, errorCode,
+				logger.error("Error while executing process at {}; code: '{}', message: {}", errorSource, errorCode,
 						errorMessage);
 
 			errorLogger.logDataReceiveFailed(getLeadingTaskFromExecutionVariables().getIdElement()
 					.withServerBase(getFhirWebserviceClientProvider().getLocalBaseUrl(), ResourceType.Task.name()));
 		}
+
+		updateLeadingTaskInExecutionVariables(task);
 	}
 }
diff --git a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/service/receive/LogValidationError.java b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/service/receive/LogValidationError.java
@@ -73,5 +73,7 @@ protected void doExecute(DelegateExecution execution) throws BpmnError, Exceptio
 					OperationOutcome outcome = (OperationOutcome) entry.getResponse().getOutcome();
 					errorOutputParameterGenerator.createCrrValidationError(outcome).forEach(task::addOutput);
 				});
+
+		updateLeadingTaskInExecutionVariables(task);
 	}
 }
diff --git a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/service/send/LogError.java b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/service/send/LogError.java
@@ -72,13 +72,15 @@ protected void doExecute(DelegateExecution execution) throws BpmnError, Exceptio
 			task.addOutput(output);
 
 			if (CODESYSTEM_NUM_CODEX_DATA_TRANSFER_ERROR_SOURCE_VALUE_MEDIC.equals(errorSource))
-				logger.warn("Error while executing local process: code: '{}', message: {}", errorCode, errorMessage);
+				logger.error("Error while executing local process; code: '{}', message: {}", errorCode, errorMessage);
 			else
-				logger.warn("Error while executing process at {}: code: '{}', message: {}", errorSource, errorCode,
+				logger.error("Error while executing process at {}; code: '{}', message: {}", errorSource, errorCode,
 						errorMessage);
 
 			errorLogger.logDataReceiveFailed(getLeadingTaskFromExecutionVariables().getIdElement()
 					.withServerBase(getFhirWebserviceClientProvider().getLocalBaseUrl(), ResourceType.Task.name()));
 		}
+
+		updateLeadingTaskInExecutionVariables(task);
 	}
 }
diff --git a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/service/send/LogValidationError.java b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/service/send/LogValidationError.java
@@ -92,6 +92,8 @@ private void addErrorsToTask(Bundle bundle, Map<String, String> sourceIdsByBundl
 
 					errorOutputParameterGenerator.createCrrValidationError(sourceId, outcome).forEach(task::addOutput);
 				});
+
+		updateLeadingTaskInExecutionVariables(task);
 	}
 
 	private void logValidationDetails(Bundle bundle, Map<String, String> sourceIdsByBundleUuid)
diff --git a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/service/translate/DownloadDataFromDic.java b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/service/translate/DownloadDataFromDic.java
@@ -4,6 +4,7 @@
 import static de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.ConstantsDataTransfer.BPMN_EXECUTION_VARIABLE_RETURN_TARGET;
 import static de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.ConstantsDataTransfer.CODESYSTEM_NUM_CODEX_DATA_TRANSFER;
 import static de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.ConstantsDataTransfer.CODESYSTEM_NUM_CODEX_DATA_TRANSFER_VALUE_DATA_REFERENCE;
+import static de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.ConstantsDataTransfer.CODESYSTEM_NUM_CODEX_DATA_TRANSFER_VALUE_ENCRYPTED_BUNDLE_SIZE;
 import static org.highmed.dsf.bpe.ConstantsBase.CODESYSTEM_HIGHMED_ORGANIZATION_ROLE;
 import static org.highmed.dsf.bpe.ConstantsBase.CODESYSTEM_HIGHMED_ORGANIZATION_ROLE_VALUE_MEDIC;
 import static org.highmed.dsf.bpe.ConstantsBase.NAMINGSYSTEM_HIGHMED_ENDPOINT_IDENTIFIER;
@@ -30,6 +31,7 @@
 import org.hl7.fhir.r4.model.Endpoint;
 import org.hl7.fhir.r4.model.IdType;
 import org.hl7.fhir.r4.model.Identifier;
+import org.hl7.fhir.r4.model.IntegerType;
 import org.hl7.fhir.r4.model.Reference;
 import org.hl7.fhir.r4.model.Task;
 import org.hl7.fhir.r4.model.Type;
@@ -61,7 +63,11 @@ public void afterPropertiesSet() throws Exception
 	@Override
 	protected void doExecute(DelegateExecution execution) throws BpmnError, Exception
 	{
-		Task task = getCurrentTaskFromExecutionVariables();
+		/*
+		 * need to use leading task not current task, since changes to current task variable will not survive
+		 * intermediate message catch events later in the process flow
+		 */
+		Task task = getLeadingTaskFromExecutionVariables();
 		String dicIdentifierValue = task.getRequester().getIdentifier().getValue();
 
 		Endpoint targetEndpoint = getEndpoint(CODESYSTEM_HIGHMED_ORGANIZATION_ROLE_VALUE_MEDIC, dicIdentifierValue);
@@ -77,7 +83,14 @@ protected void doExecute(DelegateExecution execution) throws BpmnError, Exceptio
 		{
 			byte[] encrypted = binary.readAllBytes();
 			execution.setVariable(BPMN_EXECUTION_VARIABLE_BUNDLE, Variables.byteArrayValue(encrypted));
+
+			task.addOutput().setValue(new IntegerType(encrypted.length)).getType().getCodingFirstRep()
+					.setSystem(CODESYSTEM_NUM_CODEX_DATA_TRANSFER)
+					.setCode(CODESYSTEM_NUM_CODEX_DATA_TRANSFER_VALUE_ENCRYPTED_BUNDLE_SIZE);
 		}
+
+		// see comment above on leading vs current task
+		updateLeadingTaskInExecutionVariables(task);
 	}
 
 	private Optional<String> getDataReference(Task task)
diff --git a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/service/translate/LogError.java b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/service/translate/LogError.java
@@ -56,12 +56,15 @@ protected void doExecute(DelegateExecution execution) throws BpmnError, Exceptio
 		logger.debug("Setting Task.status failed, adding error");
 
 		Task task = getLeadingTaskFromExecutionVariables();
-		task.setStatus(TaskStatus.FAILED);
 
 		String errorCode = (String) execution.getVariable(BPMN_EXECUTION_VARIABLE_ERROR_CODE);
 		String errorMessage = (String) execution.getVariable(BPMN_EXECUTION_VARIABLE_ERROR_MESSAGE);
 		String errorSource = (String) execution.getVariable(BPMN_EXECUTION_VARIABLE_ERROR_SOURCE);
 
+		// only fail if local error
+		if (errorSource == null || CODESYSTEM_NUM_CODEX_DATA_TRANSFER_ERROR_SOURCE_VALUE_GTH.equals(errorSource))
+			task.setStatus(TaskStatus.FAILED);
+
 		if (!CODESYSTEM_NUM_CODEX_DATA_TRANSFER_ERROR_VALUE_VALIDATION_FAILED.equals(errorCode))
 		{
 			errorSource = errorSource != null ? errorSource : CODESYSTEM_NUM_CODEX_DATA_TRANSFER_ERROR_SOURCE_VALUE_GTH;
@@ -71,13 +74,15 @@ protected void doExecute(DelegateExecution execution) throws BpmnError, Exceptio
 			task.addOutput(output);
 
 			if (CODESYSTEM_NUM_CODEX_DATA_TRANSFER_ERROR_SOURCE_VALUE_GTH.equals(errorSource))
-				logger.warn("Error while executing local process: code: '{}', message: {}", errorCode, errorMessage);
-			else
-				logger.warn("Error while executing process at {}: code: '{}', message: {}", errorSource, errorCode,
+				logger.error("Error while executing local process; code: '{}', message: {}", errorCode, errorMessage);
+			else // not an error if error source remote
+				logger.warn("Error while executing process at {}; code: '{}', message: {}", errorSource, errorCode,
 						errorMessage);
 
 			errorLogger.logDataReceiveFailed(getLeadingTaskFromExecutionVariables().getIdElement()
 					.withServerBase(getFhirWebserviceClientProvider().getLocalBaseUrl(), ResourceType.Task.name()));
 		}
+
+		updateLeadingTaskInExecutionVariables(task);
 	}
 }
diff --git a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/service/translate/LogValidationError.java b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/service/translate/LogValidationError.java
@@ -59,5 +59,6 @@ protected void doExecute(DelegateExecution execution) throws BpmnError, Exceptio
 				CODESYSTEM_NUM_CODEX_DATA_TRANSFER_ERROR_VALUE_VALIDATION_FAILED,
 				"Validation failed while inserting into CRR");
 		task.addOutput(output);
+		updateLeadingTaskInExecutionVariables(task);
 	}
 }
diff --git a/codex-process-data-transfer/src/main/resources/fhir/CodeSystem/num-codex-data-transfer.xml b/codex-process-data-transfer/src/main/resources/fhir/CodeSystem/num-codex-data-transfer.xml
@@ -51,4 +51,9 @@
 		<display value="Dry Run" />
 		<definition value="Boolean parameter to instruct the data-send process to abort after validating the generated transfer bundle but before transferring data to GTH/CRR" />
 	</concept>
+	<concept>
+		<code value="encrypted-bundle-size" />
+		<display value="Encrypted Bundle Size" />
+		<definition value="Output parameter describing the encrypted transfer bundle size in byte" />
+	</concept>
 </CodeSystem> 
diff --git a/codex-process-data-transfer/src/main/resources/fhir/StructureDefinition/num-codex-task-start-data-receive.xml b/codex-process-data-transfer/src/main/resources/fhir/StructureDefinition/num-codex-task-start-data-receive.xml
@@ -134,5 +134,30 @@
       <path value="Task.input.value[x].identifier" />
       <max value="0" />
     </element>
+    <element id="Task.output:error">
+      <path value="Task.output" />
+      <sliceName value="error" />
+    </element>
+    <element id="Task.output:error.extension">
+      <path value="Task.output.extension" />
+      <slicing>
+        <discriminator>
+          <type value="value" />
+          <path value="url" />
+        </discriminator>
+        <rules value="open" />
+      </slicing>
+      <min value="0" />
+    </element>
+    <element id="Task.output:error.extension:error-metadata">
+      <path value="Task.output.extension" />
+      <sliceName value="error-metadata" />
+      <min value="0" />
+      <type>
+        <code value="Extension" />
+        <profile value="https://www.netzwerk-universitaetsmedizin.de/fhir/StructureDefinition/error-metadata" />
+      </type>
+      <isModifier value="false" />
+    </element>
   </differential>
 </StructureDefinition>
diff --git a/codex-process-data-transfer/src/main/resources/fhir/StructureDefinition/num-codex-task-start-data-translate.xml b/codex-process-data-transfer/src/main/resources/fhir/StructureDefinition/num-codex-task-start-data-translate.xml
@@ -134,5 +134,64 @@
       <path value="Task.input.value[x].identifier" />
       <max value="0" />
     </element>
+    <element id="Task.output:error">
+      <path value="Task.output" />
+      <sliceName value="error" />
+    </element>
+    <element id="Task.output:error.extension">
+      <path value="Task.output.extension" />
+      <slicing>
+        <discriminator>
+          <type value="value" />
+          <path value="url" />
+        </discriminator>
+        <rules value="open" />
+      </slicing>
+      <min value="0" />
+    </element>
+    <element id="Task.output:error.extension:error-metadata">
+      <path value="Task.output.extension" />
+      <sliceName value="error-metadata" />
+      <min value="0" />
+      <type>
+        <code value="Extension" />
+        <profile value="https://www.netzwerk-universitaetsmedizin.de/fhir/StructureDefinition/error-metadata" />
+      </type>
+      <isModifier value="false" />
+    </element>
+    <element id="Task.output:encryptedBundleSize">
+      <path value="Task.output" />
+      <sliceName value="encryptedBundleSize" />
+      <min value="0" />
+      <max value="1" />
+    </element>
+    <element id="Task.output:encryptedBundleSize.type">
+      <path value="Task.output.type" />
+      <binding>
+        <strength value="required" />
+        <valueSet value="http://www.netzwerk-universitaetsmedizin.de/fhir/ValueSet/data-transfer" />
+      </binding>
+    </element>
+    <element id="Task.output:encryptedBundleSize.type.coding">
+      <path value="Task.output.type.coding" />
+      <min value="1" />
+      <max value="1" />
+    </element>
+    <element id="Task.output:encryptedBundleSize.type.coding.system">
+      <path value="Task.output.type.coding.system" />
+      <min value="1" />
+      <fixedUri value="http://www.netzwerk-universitaetsmedizin.de/fhir/CodeSystem/data-transfer" />
+    </element>
+    <element id="Task.output:encryptedBundleSize.type.coding.code">
+      <path value="Task.output.type.coding.code" />
+      <min value="1" />
+      <fixedCode value="encrypted-bundle-size" />
+    </element>
+    <element id="Task.output:encryptedBundleSize.value[x]">
+      <path value="Task.output.value[x]" />
+      <type>
+        <code value="integer" />
+      </type>
+    </element>
   </differential>
 </StructureDefinition>
diff --git a/codex-process-data-transfer/src/test/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/UcumLearningTest.java b/codex-process-data-transfer/src/test/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/UcumLearningTest.java
@@ -0,0 +1,47 @@
+package de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.validation;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertTrue;
+
+import java.io.InputStream;
+import java.nio.file.Files;
+import java.nio.file.Paths;
+
+import org.fhir.ucum.UcumEssenceService;
+import org.junit.Test;
+
+public class UcumLearningTest
+{
+	@Test
+	public void test() throws Exception
+	{
+		String theCode = "{beats}/min";
+		try (InputStream input = Files.newInputStream(Paths.get("src/test/resources/fhir/ucum/ucum-essence.xml")))
+		{
+			UcumEssenceService svc = new UcumEssenceService(input);
+			assertEquals("1 / (minute)", svc.analyse(theCode));
+			assertEquals("s-1", svc.getCanonicalUnits(theCode));
+			assertTrue(svc.getDefinedForms(theCode).isEmpty());
+			assertNull(svc.validate(theCode));
+			assertEquals("{beats}/min", svc.getCommonDisplay(theCode));
+			assertTrue(svc.isComparable(theCode, "/min"));
+		}
+	}
+
+	@Test
+	public void test1() throws Exception
+	{
+		String theCode = "/min";
+		try (InputStream input = Files.newInputStream(Paths.get("src/test/resources/fhir/ucum/ucum-essence.xml")))
+		{
+			UcumEssenceService svc = new UcumEssenceService(input);
+			assertEquals(" / (minute)", svc.analyse(theCode));
+			assertEquals("s-1", svc.getCanonicalUnits(theCode));
+			assertTrue(svc.getDefinedForms(theCode).isEmpty());
+			assertNull(svc.validate(theCode));
+			assertEquals("/min", svc.getCommonDisplay(theCode));
+			assertTrue(svc.isComparable(theCode, "/min"));
+		}
+	}
+}
diff --git a/codex-process-data-transfer/src/test/java/de/netzwerk_universitaetsmedizin/codex/processes/fhir/profile/TaskProfileTest.java b/codex-process-data-transfer/src/test/java/de/netzwerk_universitaetsmedizin/codex/processes/fhir/profile/TaskProfileTest.java
diff --git a/codex-process-data-transfer/src/test/resources/fhir/ucum/ucum-essence.xml b/codex-process-data-transfer/src/test/resources/fhir/ucum/ucum-essence.xml

Original file line number	Diff line number	Diff line change
`@@ -71,13 +71,15 @@ protected void doExecute(DelegateExecution execution) throws BpmnError, Exceptio`
`71`	`71`	`task.addOutput(output);`
`72`	`72`
`73`	`73`	`if (CODESYSTEM_NUM_CODEX_DATA_TRANSFER_ERROR_SOURCE_VALUE_CRR.equals(errorSource))`
`74`		`- logger.warn("Error while executing local process: code: '{}', message: {}", errorCode, errorMessage);`
	`74`	`+ logger.error("Error while executing local process; code: '{}', message: {}", errorCode, errorMessage);`
`75`	`75`	`else`
`76`		`- logger.warn("Error while executing process at {}: code: '{}', message: {}", errorSource, errorCode,`
	`76`	`+ logger.error("Error while executing process at {}; code: '{}', message: {}", errorSource, errorCode,`
`77`	`77`	`errorMessage);`
`78`	`78`
`79`	`79`	`errorLogger.logDataReceiveFailed(getLeadingTaskFromExecutionVariables().getIdElement()`
`80`	`80`	`.withServerBase(getFhirWebserviceClientProvider().getLocalBaseUrl(), ResourceType.Task.name()));`
`81`	`81`	`}`
	`82`	`+`
	`83`	`+ updateLeadingTaskInExecutionVariables(task);`
`82`	`84`	`}`
`83`	`85`	`}`
Original file line number	Diff line number	Diff line change
`@@ -73,5 +73,7 @@ protected void doExecute(DelegateExecution execution) throws BpmnError, Exceptio`
`73`	`73`	`OperationOutcome outcome = (OperationOutcome) entry.getResponse().getOutcome();`
`74`	`74`	`errorOutputParameterGenerator.createCrrValidationError(outcome).forEach(task::addOutput);`
`75`	`75`	`});`
	`76`	`+`
	`77`	`+ updateLeadingTaskInExecutionVariables(task);`
`76`	`78`	`}`
`77`	`79`	`}`
Original file line number	Diff line number	Diff line change
`@@ -72,13 +72,15 @@ protected void doExecute(DelegateExecution execution) throws BpmnError, Exceptio`
`72`	`72`	`task.addOutput(output);`
`73`	`73`
`74`	`74`	`if (CODESYSTEM_NUM_CODEX_DATA_TRANSFER_ERROR_SOURCE_VALUE_MEDIC.equals(errorSource))`
`75`		`- logger.warn("Error while executing local process: code: '{}', message: {}", errorCode, errorMessage);`
	`75`	`+ logger.error("Error while executing local process; code: '{}', message: {}", errorCode, errorMessage);`
`76`	`76`	`else`
`77`		`- logger.warn("Error while executing process at {}: code: '{}', message: {}", errorSource, errorCode,`
	`77`	`+ logger.error("Error while executing process at {}; code: '{}', message: {}", errorSource, errorCode,`
`78`	`78`	`errorMessage);`
`79`	`79`
`80`	`80`	`errorLogger.logDataReceiveFailed(getLeadingTaskFromExecutionVariables().getIdElement()`
`81`	`81`	`.withServerBase(getFhirWebserviceClientProvider().getLocalBaseUrl(), ResourceType.Task.name()));`
`82`	`82`	`}`
	`83`	`+`
	`84`	`+ updateLeadingTaskInExecutionVariables(task);`
`83`	`85`	`}`
`84`	`86`	`}`
Original file line number	Diff line number	Diff line change
`@@ -92,6 +92,8 @@ private void addErrorsToTask(Bundle bundle, Map<String, String> sourceIdsByBundl`
`92`	`92`
`93`	`93`	`errorOutputParameterGenerator.createCrrValidationError(sourceId, outcome).forEach(task::addOutput);`
`94`	`94`	`});`
	`95`	`+`
	`96`	`+ updateLeadingTaskInExecutionVariables(task);`
`95`	`97`	`}`
`96`	`98`
`97`	`99`	`private void logValidationDetails(Bundle bundle, Map<String, String> sourceIdsByBundleUuid)`
Original file line number	Diff line number	Diff line change
`@@ -59,5 +59,6 @@ protected void doExecute(DelegateExecution execution) throws BpmnError, Exceptio`
`59`	`59`	`CODESYSTEM_NUM_CODEX_DATA_TRANSFER_ERROR_VALUE_VALIDATION_FAILED,`
`60`	`60`	`"Validation failed while inserting into CRR");`
`61`	`61`	`task.addOutput(output);`
	`62`	`+ updateLeadingTaskInExecutionVariables(task);`
`62`	`63`	`}`
`63`	`64`	`}`